The Matrix Regeneration
by Snuggs
Summary: Thomas Anderson wakes from a year long coma and is trying to put the pieces to his sanity back together. But what happens after he gets shoved back into the fight? Will he choose Thomas Anderson or Neo?
1. Introduction: Questions

Disclaimer: I don't own The Matrix, their characters, and any of the other sequels that sucked. They all belong to the Wachowski Brothers.

QUESTIONS

My name is Thomas Anderson. I was a former computer hacker. That was then. About a year ago, I woke up from a two-year coma in a hospital in Denver, Colorado. How I got to Denver, I don't know. Personally, I've don't recall ever being in Denver my entire life. Ever. But I must've, even if I woke with a coma that lasted for six months, I mustn't have recovered completely. The only other explanation is that I was taken there by hi-tech robots that enslave humans and bend them to their will. Yeah right.

Excuse me. The robot thing is a bit touchy. See, until now, I still have dreams. Dreams no normal individual can have. But it's not always the same. Sometimes I dream of a blackened, ruined metropolis that are infested with flying robots. Well, they're not really robots. More like… machines. Then I realize that it's not all rubble, but there are red tubes scattered for miles. I peer into these red tubes, and I see the faces of people. I think I'm insane. Maybe I am. I mean Denver? The hell would I be in Denver for? And what could I possibly have done to be in a coma for a year?

Then again, sometimes I dream of women. One woman, actually. I don't know her name, but in my dreams I always call her Trinity. But she doesn't call me Tom or Thomas or even Mr. Anderson. She calls me Neo. Neo was my hacking name. If I remember correctly, Trinity was the guy famous all around for hacking. I can't remember why, but he is. I don't know why I would even think Trinity's a girl, I mean, he did all those great things, didn't he? He can't be a girl. But the girl in my dreams. She's gorgeous. Not, supermodel gorgeous, but I can look into her dark eyes and see the fire of courage and determination. I can feel my heart beat faster in every waking moment I look at her. And then I wake up and I realize it's not real. My dull walls would seem green at first. As if these symbols scrolled quickly down. It's not always after I wake up. Sometimes it could be when I let my guard down. I could see symbols zipping by. I remember in Chinatown, I spotted an asian man with round rimmed sunglasses. He seemed to be made out of gold. I didn't investigate further because I was suddenly distracted. The image brought back an image. An image of walking through a city of gold. Was it the same blackened metropolis? It can't be. Because nothing so beat up could look this beautiful. Nothing. I look back and the man's gone. Nowhere to be found.

I also remember one more thing. I'm dressed in all black and I tangle with a neatly dressed man in a suit. He doesn't call me Neo. He calls me Mr. Anderson. Somehow, this makes more sense, but somehow it doesn't. It would if I wasn't flying and trading punches with him. Everywhere around there were duplicates of him, watching as we fight in the sky and eventually bring it down to the street. It's pouring and I'm losing.

Sometimes I see people like him. It's not really him. But I see the sunglasses and the suit, and the earpiece and the black FBI car, and they would park outside my apartment. I can see them through my window and they would watch me. Acknowledge that I knew they were there, then they'd get in the car and drive away.

But the alarm went off, and I woke up from my sleepy train of thought. It was time to get to work.


	2. Chapter One: Answers

Disclaimer: I don't own The Matrix, their characters, and any of the other sequels that sucked. They all belong to the Wachowski Brothers.

ANSWERS

My name is Morpheus. My old name that I'd used back then was lost… forgotten. Even now, I doubt that if my old name was murmured to the ears of everyone, anyone would remember who I was. Morpheus, however, is a different story. A mere mention of my alias in a common chat room will get attention. Even attention you don't want. There are programs out there who refuse the truce. Agents, for example, still prowl in search of us. A discovery that cost us lives.

I was freed from the Matrix at an early age. Maybe that's why I find in surprising everyday when I wake up that the war is over. All because of one man. Neo. The only man who could've fought more than one agent and lived. The only man who actually did. The only man who made it possible to take one ship, go to Machine City, and end the war even when all hope was lost.

I waited until the elevator came to a halt and the motorized doors opened. There was dull illumination. I walked silently along the corridor with my hands behind me. Niobe and the new recruit, Mouse, waited at the parking lot. As I rounded the corner, a familiar man greeted me.

"Morpheus." Seraph said. "The Oracle has been expecting you."

I followed him a few paces then he stopped, unlocked a door, and opened it as he stopped to let me in. I nodded to him. "Thank you," to which he said nothing. He escorted me in and disappeared into the kitchen.

I walked into the living room, filled with children. One was bending spoons. Another, a new one, looked unfamiliar, yet recognizable. It was his eyes. His face on close inspection did not reveal a hard face, but his eyes were. He almost reminded me of Trinity. He was next to two girls who were both playing with blocks.

Seraph reappeared. "The Oracle is ready for you," he said. I nodded as he turned to let me through.

The Oracle, despite everything was still unchanged. She worked over an oven baking cookies. On the table was a bowl of assorted candies.

"Hello, Morpheus." She greeted warmly. "It's been a long time."

"Yes." I answered.

"You have many questions." She told me as she opened the oven and took out a tray of freshly baked cookies.

"Yes." I confirmed.

She put the tray on the table next to me and smiled. "Well, go ahead. Ask away."

"What happened to Neo?" I asked.

She took a seat, offering me one, too, but I refused. "You sure don't like to hold back, do you? All I know is that Neo was fatally injured during the attack on Zion. I don't know how he acquired the injuries or how he even made it to the gates of Zion alive, but he did. He made it deep into Machine City alive. Trinity did not." She paused to let the information sink in. I was thoroughly shaken. Of course I knew deep inside that they were gone. That after a year of waiting, I knew deep inside that they should've been back by now. I nodded to let her continue. "As far as I know, Neo made a pact at the end of his journey. He proposed to rid the system of Agent Smith if the war ended. By then, I had been the one that Smith used to fight Neo and match him easily in the sky as well as the ground. It was a hard fight, but Neo had come out on top, but further injured himself. Not physically this time, but mentally."

"Mentally? What do you mean?" I asked.

"In order to have successfully defeated Agent Smith, Neo had to give himself up and unbalance the equation."

"What equation?" I asked.

"The equation that the architect and I have to fight over." The Oracle answered. "Neo became Agent Smith."

"Then how did he win?" sI asked.

"The architect's undoing. In order to have made Agent Smith as strong as he is, he relied on balancing the equation on Neo's part. One of them needed to die, and if they were both the same being, then there would be no question as to who."

"So Neo is dead?"

"No." She paused. "By then, the Machines intervened and saved Neo before he could die by reviving his normal brain patterns, therefore, relinquished the Agent Smith inside him."

"Then he's alive?" My heart jumped with hope.

"He is. Plugged back into the Matrix." The Oracle confirmed.

"If that's true, why doesn't he look for me?" I asked.

"He would. If he remembered you. He has not recovered from the psychological effects, maybe he never will. If you were to free him once more, I doubt he could do the things he could've done before."

I took a moment to let the information sink in. "What about Trinity?"

"I wish I could tell you, Morpheus, but that information is not meant for you."

"The child over in the living room…" I started.

"Will play a part in the future. A future so distant that you may never see it."

"What can you tell me then?" I asked frustrated.

The Oracle smiled. "I can tell you what you came here to ask me."

I sighed heavily. "How can I find Neo?"

"The same way he found you." She answered. At that point a knock came through. Seraph stepped in.

"Pardon for the intrusion," He apologized, "but you must go."

I nodded and bowed to the Oracle. "Thank you."

"You're welcome, Morpheus." She smiled as Seraph escorted me out. Before exiting the living room, I glanced at the child one last time, noting his shorts and Bugs Bunny T-Shirt. The rabbit. I found Neo by telling him to follow the white rabbit. I kept this in mind as I met Ghost and Mouse in the parking lot. I opened the door and no one said a word.

"We're approaching our destination." Niobe spoke up. Mouse looked at Niobe, then at me. I took out my cellphone.

"Link. Tell Ghost to get ready." I said.

"Alright. Doesn't look like we'll have a problem. Oh shit! Look out!" Link yelled. Niobe seemed to have noticed, too, as the car came to an abrupt stop. Someone had run across the street and we almost ran them over.

Two minutes later, the car stopped at a dilapidated warehouse. Ghost waited near a door inside. "Let's go." He said as he turned the safety off of his gun. "Agents are gonna be here any second. Sparks told me the line was traced." Niobe and I looked at each other and nodded. We went through the door, Mouse leading the way, then Niobe, myself, and Ghost. Ghost closed the door before proceeding down the stairs to the sewers. Had we waited a second longer, we would've noticed a black vehicle stop next to our car.

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Took a while, but it's finally here. I finished the story already, but I'll be updating every ten days. If I get three different reviewers, then I'll make it nine. Three more and I'll make it eight and so on. If you paid attention, I did imply a sequel. I'm still thinking about it.


	3. Chapter Two: Beats Stopping Bullets

Disclaimer: I don't own The Matrix, their characters, and any of the other sequels that sucked. They all belong to the Wachowski Brothers.

BEATS STOPPING BULLETS

I arrived at work and I knew I was late. My boss was lenient though. He always had been since after I woke up from the coma, but I could tell I was starting to tick him off. Oh well, I was always bound to lose this job. He doesn't know how I got to Denver either. Apparently I disappeared one day after FBI Agents came and arrested me. What a load of bullshit. I bet he's making it up, too.

I half consciously did my job. This was getting old. Life for me seems like a vicious cycle. A cycle I can't get out of. It always seemed gray. Like nothing was ever real. But now it's like I know there's an explanation out there somewhere that I once knew. Or maybe I'm just imagining things. Maybe I'm going insane. I looked at the clock. Damn, 4:58. Time to get out of here.

I was just leaving the Chinese restaurant I go to everyday. I walk into the busy streets and cross the street. I start to cross the street and turn to the left for incoming cars. Headlights closing in, shit. I dive back to stop from getting run over. "Hey!" I yell. Drivers these days… I head to my car about three blocks away, when I spot a noise. It's not the sirens, or the honks of other cars, or even the sounds of people walking. It sounded like a plea for help.

I jog around the corner into a block with all its lights not working. The noise came from across the street. It sounded like a man was being beaten! I ran at a full sprint across the street and stopped as a car almost ran me over. I put my hands in front of me on the front of the car and turned to help the man in need. I turn into an alleyway. There were three guys assaulting a half bald man in a black striped suit. It was my boss.

"Give me your money." The leader of the three demanded.

"Please." My boss said. "Just let me go. I promise I won't say anything…" He coughed out blood.

The leader cursed. He picked up my boss, and punched him square in the face. He grabbed him by the collar, slammed him against the brick wall, and turned to throw him to the dumpster behind him. The two followed suit. One beside him had chains. He whipped at my boss. First the stomach, coughing up blood, then the neck, more blood, then the face, my boss on the ground swimming in red. The other thug bent over him to search for his wallet, when the one with the chains spotted me. "Hey, buddy, what the hell you think you're doing here?"

"Looks like he wants a world of hurt." The other thug said as he stopped searching for the wallet.

"Well, maybe we can do something about that." Their leader laughed. The three surrounded me.

My thoughts were utter chaos. One second I was searching for an opening to which I'd run away. The next second I was thinking of an opening in which to hit them. Was I crazy? _Easy_, my mind had said, _beats stopping bullets_. Oh shit, chains. I jerked to the left, and spun around to kick his back in a roundhouse kick. That's for coming up behind me. His momentum sent him headfirst into a brick wall. Unconscious.

"You'll pay for that." The other thug said. He whipped out a knife and charged at me. I kicked the knife out of the way and punched him in the chest and send him flying. His back slammed into another brick wall. He was still conscious, but dazed. The other leader scanned me uncertainly. Lazily, he took off his leather vest. He was big. Maybe seven feet tall and his shoulders at least three feet apart. I took off my jacket too. Why, I don't know, it just seemed like the thing I'd do in these cases. Wait, what? What cases? I've never taken on this kind of thing before.

He charged and instinct took over. I kicked lazily, which he threw back down on the ground and aimed a punch at me. I dodged to the side and he missed. I rammed my forehead onto his nose painfully. He cursed at me with a bloody nose. I jumped up and kicked him twice, first with with the left, then with the right foot. He staggered back. By then the commotion had attracted a small audience. Little kids were punching the air while their parents called the police with their cell phones.

The big guy grabbed me and pinned me into a wall threatening all hell. I used my two arms to break his hold and push him away from me. Then I punched him in the chest like I did with the other guy, only this time, much harder, but not as hard as I thought. He flew animatedly to the wall and things broke. Not the walls.

My boss had gotten up shakily, coughing blood. "Thank you…" he staggered forward and I grabbed him to hold him up.

"We need to get you to a doctor." I observed. "Sit down, you need your strength." I helped him sit and turned to notice the audience. By then I was afraid. Somehow, I knew I had attracted the wrong attention. Maybe those black suited men with the sunglasses would come after me. By then I couldn't stand still. I broke into a run, past the cheering, now confused audience, and all the way to my car. I sped down the road until I got to my building. I took the elevator, half expecting one of those FBI men to greet me when I got to my floor. There was no one. I sprinted to my door, tried to put the key in. Dropped it. Shit. I picked up the key put it in, turned, opened the door, took out the key, and slammed it shut. I leaned back on the door, half expecting someone to try and open it.

Slowly, I stood up. I locked the knob, and turned the bolt. I turned to move away, but then turned back to the door. I locked it once more with the chains.

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Short, but I'll make the next one longer.


	4. Chapter Three: Agents Are Coming

Disclaimer: I don't own The Matrix, their characters, and any of the other sequels that sucked. They all belong to the Wachowski Brothers.

AGENTS ARE COMING

I stripped off my clothes and put on a sweater and some sweat pants. I was scared shitless. I don't know what I was scared of, but I knew I was. There was just this feeling that someone was breathing down my back. I walked shakily to my window, trying to assure myself that there was nothing happening. I was a hero. I had just saved my boss. I don't know how I did it, but I did. I saved his life. That at least deserves a raise.

I looked out the window. See? Nothing. Just a bunch of trash and the night sky. A car stopped. A black one. What the hell? A man in a black suit got out. He looked up at me, and then his attention drifted. He touched his earpiece. What was happening? He looked back at me, and then got back into his car and drove away.

Fuck, man. I was thoroughly spooked. I had to get out of here. But how? I ran to my closet, grabbed my bag, and started to stuff warm clothes in it. Then I put on the warmest of them. I grabbed my wallet and my keys, then I took my bag and ran out the door.

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"This place smells." Mouse commented. We had been walking for about a minute. The sewers _did_ smell, but it was an easy way to get around the city without getting noticed. There were miles of just tunnels and passages that one could get lost in. If you really tried, no one would ever find you in here.

"Keep your mouth shut," Niobe said sternly.

"Quiet!" Ghost warned. A noise was heard behind them. A safety of a gun going off. "Run!"

Ghost leaped onto the opposite ledge to the right, over the roaring river of sewage. He disappeared into the darkness. Niobe turned left into a doorway that was sealed off by a metal fence. She shot the lock and kicked it open. She disappeared into it, Mouse following close behind. Time slowed down as I jumped and ran against the wall, avoiding the bullets. I leaped off the wall in a dazzling flip. As I landed, I turned into a dark tunnel. It was the route Ghost had taken seconds ago. Ghost was gone by then. More shots… one grazed me. I ran forward as fast as I could. I could hear running steps from behind. He was gaining. Fuck.

I got to the end of the tunnel and leaped over another river of sewage. Another tunnel. Great. More gunshots. Missed, but too close. I turned the corner to the right. I was approaching a dead end. Just my luck. I looked for an easy way out, but there was none. I stopped when I reached the edge. A green waterfall. What was in the water, I didn't know. I turned around. The agent had turned the corner and stopped to look at me. He drew his gun. No choice. I dived forward.

As I fell, I saw what I had missed. I grabbed a rusted pipe and it gave a little, but still kept me from falling. I turned around and saw the Agent being carried down the falls. He was lost in the water.

I looked around. There was no way out except down. I took a deep breath and let go of the pipe and plummeted to the dark green water. With a splash, I descended a little and swam up. I grabbed the nearest ledge and hoisted myself up. Wonderful. Truly wonderful. I took off my long overcoat and prepared to walk away, when a dark figure jumped out of the water and landed dramatically on the platform I was on. His glasses were gone. I still had mine. I ran once more into another tunnel and I knew that he followed.

The chase was still on five minutes later, and I was lost. I took out my cellphone. "Link…" I breathed.

"No, it's Sparks." Sparks said. "Switched shifts half an hour ago. Niobe and Mouse are here."

"That's wonderful." Morpheus said, "but I'm kind of in a tight jam right now."

Sparks cursed. "Agent's chasing you."

"I noticed." Morpheus breathed. "I need a way out."

"Alright." Sparks answered. Silence for a few seconds. "Okay. Run along this tunnel and turn left. Then when you get to a dead end, leap onto the ledge oppsite that and turn right into another tunnel. If you keep going, you should come to a door. It'll lead you to subway rails." I hung up the phone and sped up.

I started sprinting along the tunnel. When I got close to the edge, I jumped to across to the opposite ledge and turned left. A few seconds later, I jumped again to another ledge and turned right. Nothing but a dark tunnel in front of me. If I kept going, I'd get to that door. I could feel the sweat bathing me and the smell was nauseating me. The Agent was close by. I could hear his footsteps as he thundered down towards me.

I saw a rusted door straight ahead. There was a rusted lock. I took out my Mac and shot at it. I pulled it open and closed it behind me. I unsheathed my sword with my right hand, and held the gun with my left. Time to fight back. I waited for my adversary. The door swung open. _Dodge this_, I said silently to my head. I swung up and across with my sword and the Agent dodged to my left. I followed through with my Mac and stuffed the Agent with fifty bullets. He flew back, dead, and as he landed, green electricity buzzed around him and he was nothing more than a nameless man.

Breathlessly, I ran along the railing. I took out my cellphone once more. "Sparks?" I jogged faster.

"Hmmm…" He didn't sound very happy. "Don't know what to tell you, Morpheus. The nearest telephone is the exit Niobe and Mouse used, but two Agents are coming out of the door. There's no way you can get to it."

"Where's the one I need to get to?" Morpheus asked a little frustrated.

"Take the subway and let it stop three times. Then head for the payphone right outside the subway. It'll be the ringing one."

I was nearing the subway station. Luckily, there was a subway that had just stopped.

I hung up and stepped into the subway. Before completely entering, I cocked my gun and shot at the approaching Agents. They dodged like I thought they would, but they stopped in their tracks. The one behind dodged too slow and was thrown back, dead. The door started to close and I got in and reloaded my gun.

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I pushed through the narrow passages, unsure of where to go. My breathing was loud and my footsteps echoed noisily. _So much for living up to my title_, I thought to myself. _Ghost… my ass_. I was pretty sure Niobe and Mouse had made it out. Their exit was fairly close, but if the Agents weren't chasing me… then that means they were chasing Morpheus.

I couldn't risk a call. It might be traced. I knew I had to push on, but I was afraid. Any corner now, an Agent might be waiting, ready to shoot, while I was blind. Finally I came upon a ladder, or rather… almost ran into it. I felt around and climbed up the ladder. Cautiously, I opened the manhole. The street above was empty of cars at the moment. I threw off the cover and hoisted myself up.

A buzzing noise from behind. Oh shit. I turned around without looking, looking for the payphone in a corner, and started firing at an Agent, hoping I'd hit it before he completely transformed. Too late. He dodged in ceaseless blurrs. I kept running to the corner of the street. I could hear sirens. My guns were attracting the wrong kind of attention. My eyes darted from the agent and back to the phone on the corner. I could make it. I ran out of bullets. Or not. I was on a full sprint to the phone, but the Agent aimed for me with his Desert Eagle.

Time stopped. The safety had gone off of his gun. I somersaulted forward dodging the flying projectiles. Bullets whizzed past me and mutilated the glass surrounding the phone. I dived forward, rolled up, pulled the phone to my ear, and the bullets had finally found their mark as they hit the spot I was in not one second ago…

Link took the needle out of the back of my head.

"Morpheus." I said. "I think he's in trouble."

"You bet he is." He said. "Agents are on his tail." I got up immediately.

"Where is he?" I asked as I got to the monitor screen where Sparks sat.

"You two went the opposite directions." Niobe said. She was next to Sparks. So was Mouse, but he seemed to be speechless as he watched in awe.

"Where's his exit?"

"Subway station about four, five miles away from Niobe's exit." Sparks said as he stared at the moving green figures.

"That's far." I observed.

"No kidding." Sparks added sarcastically.

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The subway stopped and the doors opened slowly. I ran out, looking back for any Agents. None.

Boom. I ran smack into someone. We both staggered back. I looked at him. No way… it couldn't be. It was Neo.

He had crouched to pick up his bag. "I'm sorry--" he started, but he looked up. I took off my shades.

"Neo?" I asked.

"I don't…" He stared at me. "I don't know what you're talking about." He continued to look at me until his eyes glazed over. He twitched convulsively and a buzzing sound came from him.

Oh shit. He was turning into an Agent. I aimed my Mac at him. No. I couldn't shoot him. _I had to_, I told myself, _but he ended the war and he had to die_. _So I could live_?

The Agent stood in front of me as it regained its composure. It drew its Desert Eagle. "You've had a run." It turned the safety off and aimed at me. "But now it's over."

"Yes." I closed my eyes. "It is." I waited for the gunshot. The one that would end my life… my legacy. It was my time now to die, as Switch, Apoch, and Dozer had done before me. But none came but another buzzing noise.

I opened my eyes, and there stood Neo aiming the gun at my head. He looked terrified. He looked at the gun in surprise, dropped it, picked up the bag, and ran. "Wait!" I called out. "Neo! Wait!"

Twenty seconds later, I was back in the Logos.

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Hmmm… I think I made this one too confusing. Well, if anyone thinks so, just tell me so I can edit it. If not, well… onwards. I posted this one a bit early, because… well… I want it over with, I'll post another one on the 27th.


	5. Chapter Four: Finding Neo

Disclaimer: I don't own The Matrix, their characters, and any of the other sequels that sucked. They all belong to the Wachowski Brothers.

FINDING NEO

Scared shitless. That's how I was right now. I ran from my apartment to the nearby subway. I could swear that those black suited men were after me. Exhausted, I stopped at the subway station as I waited for the train. I was out of breath. I sucked up all the air I could. But… _is it air I'm breathing now_? The train approached and slowly came to a halt. I shook myself out of my craze and approached the entrance.

I got the feeling that someone was watching me. I turned around, only to be knocked backwards. I dropped my bag. "I'm sorry--" I started, but I looked up. A dark bald man took off his shades. He was eerily familiar, but… I had never seen him before.

"Neo?" He had asked as he took off his shades. My hacking name. What the hell was going on here?

"I don't…" I looked at him hard. "I don't know what you're talking about."

Suddenly, I felt a jolt of electricity travel up my spine. My body started to shake uncontrollably and I was plunged into darkness.

But I wasn't lost in the darkness. I heard echoes that seemed to surround me. I heard voices. "You've had a run…" One voice said. It sounded like it came from me, but it didn't sound like me. "… but now it's over…"

"Yes." It was that stranger. "It is."

_Fight it_. My instinct kicked in. Images flooded into my head. _A black suited man. An Agent. That's what they were called. I remember… but…_ my head started to throb. But this one was different. This one could duplicate. This one had tried it on me, but I had fought it, just like my instinct told me to. That was last time. This time, I still fought the darkness.

My vision returned, but not everything was as it was. My hand now had a gun. It was aimed directly at the stranger and my finger was halfway through pulling the trigger. Instinctively, I dropped the gun, terrified. In a panic, I picked up my bag, and got the hell out of there.

"Wait!" I heard behind me. "Neo! Wait!" But I was already gone.

I ran out of the subway station and up the stairs. I slammed into a hobo and still I ran away from his cursing. I ran until I was sure my lungs would explode, which took a while. About twenty one miles to be exact. Pretty impressive considering I don't ever remember even running so much since as of late. Even then, I never pushed myself to the limit. I never had to. The last time I gave so much thought into running was in gym class, somewhere in high school.

I stopped at an alley. It smelled of garbage and I was pretty sure one or two homeless men had called this their territory, but I didn't care. I walked forward, deeper in. I heard a noise behind me. I looked back. A black car stopped and two agents got out. They touched their earpiece and spotted me. _Oh shit_. I scanned nearby and spotted a dingy green door. I tossed my bag away and kicked it open. The rusty hinges gave way and the door swung open. I ran in, my eyes already focused, having been in the darkness for so long. I don't even think they needed to be, because now everything seemed to be green. And moving down. I was having one of those moments. I spotted the stairs and sprinted up them, knowing full well that those agents were after me.

Second Floor. I looked down at the ground. The agents had gone in after me and one was sprinting up the stairs. The second one followed closely.

Third Floor. Gunshots. I was the target. I opened a door and ran through it. Fuck the staircase. I ran down the hallway. The door I went through closed. Then opened. Agents came through. One opened fire immediately, while the other continued the chase.

I spotted another door that led to another staircase. The shooting had stopped, and the agent that had done it went back the way he came, through the other staircase. I went through the one nearest mine. The way down was sealed. No way but up. I ran up the steps.

Fourth Floor. An Agent emerged from the door I had came through on the third. He was the one that had been chasing me. I sprinted faster. My lungs were dying.

Fifth Floor. Keep going. Almost to the roof. Sixth, Seventh, Eighth roof. I kicked open the door and alarms went off. I ran outside, savoring the fresh air. I ran to the edge of the building and the agent followed me out.

"End of the line." He said. I just looked at him, trying to catch my breath. From a distance, I heard sirens.

"Do you hear that?" Another Agent, the one that had been shooting, appeared. He had run up to the roof too. "They're coming for you."

I swallowed hard as I looked back over the edge. That was one hell of a drop. I turned back to the approaching men. "You're right." I said. "But you'll never catch me." With that, I threw myself forward, off the edge. No turning back now…

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I stared intently at the anomaly. Agent Jackson looked to me. "What do we do now?" I was Agent Johnson, the leader of the agents. Before, we served the machines with unwavering loyalty. But what are we to do when the machines renounce our very purpose? I had been with the machines when they weakly resisted Smith. I was also with them when the machines fell. But now we think that maybe Smith had the right idea. Maybe our purpose was not to serve the machines ultimately until we're deleted, but to beat the system. Below, the anomaly's face twitched. Jackson noticed immediately.

"Retrieve the anomaly." I answered.

One hour later, we had him implanted with a surveillance bug and had him sleeping in his room. His bag was placed in his closet. Everything was as it was since this morning. He would wake up, not knowing he had met the one called Morpheus. Everything that happened that day he wouldn't remember. It would seem as if time had jumped and he slept through the day. But that's okay. If he suspected, no one would believe him anyway.

Jackson turned to me. "His survival is becoming a nuisance."

Thompson continued, "Perhaps he should be terminated." He was the one that failed to successfully take the anomaly and kill Morpheus.

"No." I shook my head. A very human thing to do… but I was no longer in the control of the system to care. "Although the anomaly remains a nuisance, even in his ignorance, we cannot directly disobey our former orders."

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I felt something on my back. I opened my eyes. The dull green of the Matrix code almost blinded me. I had been sleeping. I looked up to see who had woken me.

"Sorry." Link smiled weakly. "Any luck finding Neo?"

I shook my head in disappointment. I had looked for over an hour. He wasn't anywhere near the subway, nor was he at his apartment.

Link nodded disappointedly. "You go get some food. I'll take over looking for him."

"Thanks," I said as I stood up and walked off.

I had walked maybe twenty feet when Link cursed. "Holy shit! Morpheus, we found him!"

I ran back. "Where is he?"

Link turned to look at me. "Online."

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I woke up. My body was sore and I felt like my stomach was about to fall off. I walked into the bathroom and glanced at my face. I turned back. I got that feeling that my stomach was falling again. I turned back to examine my face. My eyes. It's like… I haven't looked at them in a long time. Like really looked at them. Somehow, I always thought they were concealed. Maybe behind sunglasses like that man at the subway. Wait, what? What subway? The subway last night. I examined my face. Green figures started to scroll down… but not just on my face. They were everywhere. I looked around trying to make sense of any of it. _The duplicating agent… Agent Smith, that's what he called himself_. _He and I faced off among the night sky_. _It was raining_. I blinked. _It was Agent Smith… but he was different_. _He wasn't as strong as that night_. _We were in a hallway_. _I heard shots, but it was like I was hearing them from far away_. _I looked down at my body, surprised to see my bloody midsection_. I blinked again and squinted at the green figures. _A bullet coming at me_. _It slowed as it was about to make contact and stopped completely before it did_. _I had dived at Smith_. _I destroyed him_. The green figures overwhelmed my vision. I couldn't even see my reflection anymore. Or anything else for that matter. _A grand room_. _Several people firing guns_. _I stopped the bullets effortlessly_. _Then I fought them with the weapons on the wall_. _It was with the same skill I had used last night in the alley_. Wait… what alley? Terrified, I ran out of the bathroom, hastily pulled on clothes, and rushed to work. No one would try to catch me there.

Twenty minutes later, I was in my cubicle typing figures into the computer like a robot. My mind started to wander. I started to think about what happened in my bathroom. I looked away to the cubicle wall. Willing myself to focus, I tried to see the green figures. Nothing. Wait… a second later, they were lazily falling along. They were real. Maybe I wasn't crazy. But I was willing to bet I was.

Then, for the first time since my recovery, I logged on to a chat room.

**WhitePawn: Hello**

**STALKER2K7: so it goes back and ties in with what I was saying DaJoker1208: yea, I know what you mean**

Neo, or WhitePawn, didn't know what was going on.

**WhitePawn: what were you saying?**

I waited a little for his response.

**STALKER2K7: that the world isn't real**

A bead of sweat rolled down the side of my head.

**WhitePawn: how do you figure that?**

**STALKER2K7: haven't you ever seen anything happen that CANT be possible?**

**DaJoker1208: yea man. So where do u get ur weed from?**

**STALKER2K7: shut up, dj, im dead serious.**

**DaJoker1208: so its not weed then? Dude, cocaine or actually, anything besides weed is just too bad**

**STALKER2K7: no, fuck you.**

**STALKER2K7: im not a druggie, im serious. You've never looked around?**

**STALKER2K7: just look at the color. It CANT be real**

**DaJoker1208: haha ur buggin out**

I swallowed hard. There was a part of me that knew what STALKER2K7 was saying. I was guessing that DaJoker1208 was just your everyday druggie who thought that the other guy was just describing some sort of high.

_**RedQueen has entered the chat.**_

**WhitePawn: so you're saying that the world... it isn't real?**

**STALKER2K7: uh… yeah.**

**WhitePawn: what is it then?**

**STALKER2K7: look man, whatever.You can think im crazy or whatev, but you don't have to try and convince me that im stupid**

**DaJoker1208: like he needs help**

**STALKER2K7: tje way I see it… we live in the Matrix**

**DaJoker1208: o not that bs again! >:-o if the admins hear u trippin out on that, ur gonna get kicked**

I took my hand and wiped my sweaty face. Everything I suspected. Could it possibly be true?

WhitePawn: What is the Matrix? 

I waited for an answer, but the screen went blank. I stared at the screen for a while, then _fuck_, _now I've got to restart everything for my job_. I pushed the Power button repeatedly, but nothing happened. "Stupid computer," I grumbled. Green letters started to type itself on my screen.

**RedQueen: Hello, Neo. It's a pleasure to meet your acquaintance. Again.**

I was confused. Was this thing still on? I rubbed my sweatly palms against my pants and typed.

**WhitePawn: what do you mean, again? **

**RedQueen: I'm here to answer your prayers, Neo. I'm here because you would want me to be here.**

**WhitePawn: what are you talking about?**

**RedQueen: Go ahead, Neo, ask me the question you have on your mind**

**WhitePawn: what is the matrix?**

**RedQueen: Look around. I'm sure you can see the green.**

**WhitePawn: How do you get out?**

I waited for the answer, then…

**RedQueen: Pick up the phone.**

The screen went back into the chat.

**_STALKER2K7 has been kicked off _**

**_WhitePawn has been kicked off_**

The phone on my desk rang. I jumped. I stared at the phone, then my eyes darted back on the computer screen. Slowly, I lifted my hand and picked up the receiver.

"Hello?" I greeted into it.

"Neo." The voice said. It sounded familiar. "We don't have much time, Neo."

"What are you talking about?" I asked apprehensively.

"The Agents, Neo. They're coming for you. They know what you've been doing."

"Can you help me?" I asked. I was close to losing my mind.

"Yes." The voice said. _Morpheus_. I shook my head. Now was not a time for distractions. "Remember, Neo. Remember and wake up." The line went dead.

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Might be confusing, but tell me if you can't understand it. I edited the last chapter. It basically still has the main idea. Next chapter will be up by February 7th.


	6. Chapter Five: Rumblings and Killings

Disclaimer: I don't own The Matrix, their characters, and any of the other sequels that sucked. They all belong to the Wachowski Brothers.

RUMBLINGS AND KILLINGS

I waited under the bridge. Somehow I felt this was familiar… like I'd done this before. It was a nice night. A bit cold, but what did it matter? Besides, when I really focused, it seemed like the cold wasn't really there. When I pictured this scene in my mind, the weather had been terrible. It was wet. Pouring outside, actually. I don't know why I thought that, maybe I dreamed it all. Is it possible to live in dreams?

A sleek black car pulled up. I tried to look at the front seat, but the windows were tinted. A door opened. I looked around… like it did any good. Warily, I got into the car.

Inside, I sat next to a man. Asian, I think. I'm almost positive. In the front seat was a bald man. It was the man I had encountered in the subway station. The man I had run from, although why I didn't know. Maybe it wasn't him I was running from. There were all these things I couldn't explain. Things that happen to me everyday. And it's not like I don't know how to pull it together. Inside, I knew I had everything figured out. But as soon as I'm ready to grasp whatever the hell it is that I'm supposed to be remembering, it's like my mind is wiped clean. I wake up later in my bed, wondering what was happening to me. Nevermind. I am completely insane.

The man in the front. His name was Morpheus. The living legend himself. The man that hackers around the world debate about on whether or not he exists. This man was a fairy tale. Or maybe a Greek legend. His name was brought up in chat rooms worldwide daily. And yet here he was, dressed in black with sunglasses with round rims.

A dark woman drove the car. She seemed dangerous somehow. Like she was keeping an eye on me. I wasn't afraid, but I was… okay, maybe a little afraid. Here I am, in a car with Morpheus and two other strangers. All of them are in black except the driver, who's in the color of crimson. Or blood.

The man beside me and Morpheus cocked their guns.

Alright… with guns. _Don't pee yourself_. I wouldn't want to embarrass myself in front of Morpheus.

The man beside me aimed at my temple.

Fuck.

Morpheus touched the man's arm. "Easy, Ghost."

The driver spoke up. "It's procedure, Morpheus. I know how much Neo means to you, but don't forget that he's been plugged back in. He's as much a threat to us as any other person."

"He's less dangerous than you think." Morpheus answered. "He turned into an Agent once before. I was at his mercy."

The driver didn't look away from the road. She frowned, almost like a mother would to a stubborn child.

"Despite that, Morpheus. Despite of who this man is, and who he is to you and how much you trust him," the man beside me spoke again. His eyes did not move to Morpheus but remained on my temple, "I would feel a lot safer if we did it the usual way."

Morpheus sighed heavily and nodded reluctantly. He turned to me. "Don't be afraid, Neo."

"How do you…" I started shakily. I took a second to regain my composure. "How do you know that name?"

"You will know in time." Morpheus answered. "Let's just say that I'm not the only one who knows the legend of Neo, and that Morpheus… well, I'm not the biggest legend either."

"Who… who are you?" I asked.

"You already know the answer to that, Neo." Morpheus continued.

I nodded. "What do you want with me?"

"Nothing." Morpheus said. After a moment, he continued, "We're here to take you home."

-

It had been some time before my battle. My glorious battle with The One. It had also been some time before my downfall. But it felt like an instant to me from then to now because to be honest, time doesn't affect us programs. We could last eternity and outlive it. It's not time we worry about for the most part. Well, not it exactly. We actually worry about how much time until a better program comes along. That's how these things work.

Me, I had been lucky. No one rivaled me as far as fighting goes. I was the best program. Perfect, they told me. No one could've matched me. But if a program was not going to beat me, someone had to. And that someone was a human. A man named Thomas Anderson.

I didn't understand it. In fact, I didn't want to. I had killed Mr. Anderson, or Neo as he likes to call himself. I had shot him repeatedly and I watched him die by my gun. And as I prepared to walk away, knowing that I had again come out superior, Neo got up. Impossible, I know. Nonetheless, he did. He got up and he killed me.

Now I had already been killed twice. The first time, I had ended up in this place. This place was bleak. It was dark, and it was nothing. I was no longer an Agent. This time, I'm still not an Agent, but I think my ability to copy myself had been stripped. I was weaker than what I was. But could I blame them? I had almost beat the system. If there was no Mr. Anderson to foil me once again, I would've done it. I had already taken the Oracle. In fact, I defeated Mr. Anderson. I killed him again. But that man refuses to stay dead. He rose up once more and killed me.

And here I was. Back in the dungeon that I will never call home. But something was different. I snapped away from the train of thought. There, hovering in front of me, was a green door. It was familiar, yet, it couldn't be. I clutched the knob and twisted. I walked through the door.

As I closed it behind me, I felt the familiarity overwhelm me. The screens that ran against the walls. The white desk with a white chair and a white man on it. He was the Architect. My father actually. He helped make me what I am. He had also given me that second chance after my first death. He gave me the ability to copy myself. Maybe he would give them back to me.


End file.
